Genomics in Mountain View: A Visit to 23andMe and Complete Genomics

Apologies for the blogging drought over the last few weeks – a combination of travelling, job-hunting, workload and other time demands has thoroughly devastated my writing time. I’m hoping to get back on track over the next week or so, and in particular to refocus on the ongoing controversy surrounding the future regulation of personal genomics.

In the meantime, I wanted to share some photos I took during a trip to San Francisco a few weeks ago, when I got a chance several of my favourite companies. Firstly, here’s the unassuming front entrance to personal genomics company 23andMe, in a block of commercial buildings tucked between the sprawling Googleplex and the Nasa Ames Research Center:

I was graciously received by Shirley Wu, who gave me the grand tour, and various members of the 23andMe science team (especially Nick Eriksson and Tom Do) then uncomplainingly put up with my questions for what must have seemed like hours. The visit reinforced my overall impression of the company: this is a group of very smart people working with an increasingly impressive customer data-set on some seriously interesting problems. Their recently announced discovery of two novel genetic regions associated with Parkinson’s disease (due for publication in the near future) is a taste of what’s to come.

Here my questions were patiently and expertly answered by Jennifer Turcotte, Mark Sutherland, Geoff Nilsen and Bruce Martin. Turcotte also gave me the tour of the facility, finishing outside the famous “blue room” where Complete does its sequencing:

The blue light isn’t just for visual effect – normal fluorescent bulbs would interfere with the sequencing process. However, it certainly does make for a visually striking scene.

Two surprising features of this room that aren’t apparent in this photo: firstly, it’s small, amazingly so given the machines in this room currently have the capacity to churn out 400 complete human genomes every month. Secondly, the machines really aren’t pretty. In fact they’re a testament to raw functionality, designed to have easily accessible components rather than a gleaming exterior (unlike, say, the notoriously ostentatious Pacific Biosciences instrument). That’s exactly what you’d expect: Complete’s business model doesn’t involve selling instruments, but rather relies on providing a centralised factory churning out sequence data for external customers as quickly, cheaply and accurately as possible.

When Complete launched in February 2009 the company faced skepticism – bordering on outright hostility – from the genomics community. That has since largely melted away in the face of genome sequences that are certainly comparable in quality (if not superior) to those generated using other short-read sequencing technologies; if you’re into this kind of thing, you can see for yourself using the company’s public release of 60 genomes.

In addition, general skepticism that a service model could work for genome sequencing has dissipated. As whole genome sequencing starts to become routine, the idea of out-sourcing that task in order to focus on more experimental technologies has become more appealing for large genome facilities. For smaller labs without the capital to invest in large-scale sequencing infrastructure, Complete provides an appealing option for small-scale disease genomics projects.

Since Complete launched my opinion of the company has improved on a strong and roughly linear trajectory; this visit made the gradient of that line substantially steeper. This is a deeply impressive outfit, and you’ll be hearing a lot more about Complete (from me and others) over the coming months.